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The youthful boy cries out as his skull is firmly gripped, a large thumb digging into his cheek as his parent's powerful hand holds him by the neck. That moment from Abraham's Sacrifice visits the Uffizi Gallery, creating unease through Caravaggio's chilling rendition of the tormented child from the scriptural narrative. The painting appears as if Abraham, commanded by the Divine to kill his son, could break his neck with a single twist. However Abraham's preferred approach involves the silvery grey blade he holds in his remaining hand, prepared to cut Isaac's neck. A definite element stands out – whomever modeled as Isaac for this breathtaking piece demonstrated extraordinary acting ability. Within exists not just dread, surprise and begging in his darkened gaze but also deep grief that a protector could abandon him so utterly.

The artist took a familiar biblical story and made it so fresh and visceral that its horrors seemed to happen directly in view of the viewer

Standing before the artwork, viewers identify this as a actual countenance, an precise depiction of a young model, because the identical youth – recognizable by his tousled locks and nearly black eyes – appears in several additional paintings by the master. In each case, that richly expressive face commands the scene. In John the Baptist, he peers mischievously from the darkness while holding a ram. In Victorious Cupid, he grins with a toughness acquired on Rome's streets, his dark feathery appendages demonic, a unclothed child creating chaos in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a British museum, represents one of the most embarrassing artworks ever painted. Observers feel totally unsettled looking at it. The god of love, whose darts inspire people with often painful longing, is portrayed as a extremely real, vividly illuminated nude figure, standing over overturned objects that comprise stringed instruments, a music score, plate armour and an architect's ruler. This pile of possessions resembles, deliberately, the mathematical and architectural gear scattered across the floor in the German master's engraving Melencolia I – save here, the gloomy disorder is caused by this smirking Cupid and the turmoil he can release.

"Love sees not with the eyes, but with the soul, / And thus is winged Cupid depicted blind," wrote the Bard, just prior to this painting was created around 1601. But Caravaggio's god is not blind. He gazes straight at you. That countenance – sardonic and ruddy-faced, looking with brazen assurance as he struts unclothed – is the same one that shrieks in terror in Abraham's Test.

As Michelangelo Merisi da Caravaggio painted his three images of the same unusual-looking kid in the Eternal City at the start of the 17th century, he was the most celebrated sacred painter in a metropolis ignited by Catholic revival. Abraham's Offering reveals why he was commissioned to decorate sanctuaries: he could adopt a biblical narrative that had been depicted numerous times previously and make it so fresh, so raw and physical that the horror seemed to be happening directly before the spectator.

However there existed a different side to Caravaggio, apparent as soon as he arrived in Rome in the winter that ended 1592, as a painter in his initial 20s with no mentor or patron in the urban center, just talent and audacity. Most of the paintings with which he captured the holy metropolis's eye were anything but devout. What may be the very earliest hangs in the UK's National Gallery. A young man parts his crimson mouth in a scream of agony: while reaching out his filthy digits for a fruit, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid squalor: observers can discern Caravaggio's dismal chamber mirrored in the cloudy liquid of the glass vase.

The adolescent sports a pink blossom in his coiffure – a emblem of the sex trade in Renaissance art. Venetian painters such as Titian and Jacopo Palma depicted courtesans grasping flowers and, in a work lost in the WWII but known through images, Caravaggio represented a renowned female prostitute, holding a posy to her chest. The meaning of all these floral signifiers is obvious: intimacy for sale.

How are we to make of the artist's sensual depictions of boys – and of a particular boy in specific? It is a inquiry that has split his commentators since he achieved widespread recognition in the 1980s. The complicated historical truth is that the painter was not the queer hero that, for example, Derek Jarman presented on screen in his 1986 film Caravaggio, nor so entirely devout that, as some artistic scholars improbably claim, his Boy With a Basket of Fruit is actually a likeness of Christ.

His initial paintings do offer explicit erotic suggestions, or including offers. It's as if the painter, then a destitute youthful creator, aligned with the city's sex workers, offering himself to survive. In the Florentine gallery, with this thought in mind, viewers might turn to another initial creation, the sixteenth-century masterwork Bacchus, in which the deity of alcohol gazes coolly at the spectator as he begins to undo the black ribbon of his garment.

A few years after the wine deity, what could have motivated the artist to create Victorious Cupid for the art patron the nobleman, when he was at last becoming nearly established with prestigious ecclesiastical commissions? This unholy pagan god revives the sexual challenges of his early works but in a increasingly powerful, uneasy manner. Half a century later, its secret seemed obvious: it was a representation of the painter's companion. A British visitor viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] owne boy or assistant that slept with him". The identity of this adolescent was Francesco.

The painter had been deceased for about 40 years when this story was documented.